Varys was born in Lys as a slave. He served as an apprentice to a troupe of mummers, who travelled around the Free Cities, Oldtown and King's Landing. During a stay in Myr he was bought by a man. He was given a potion by the man that paralysed him, but did nothing to dull his senses. He then cut away Varys' manhood by the stem before throwing it in the fire.

The man then told Varys that he should die, throwing him out on the street. Varys determined to stay alive out of spite. He resorted to prostitution and thieving as a way to survive, soon becoming the best thief in all of Myr.

He was then forced out by a rival and forced to flee to Pentos. It was here that he met the young sellsword known as Illyrio Mopatis. There they struck up a deal, with Varys stealing information and then Illyrio saying that he would retrieve it for his patrons.

Varys gained an infamous reputation in the Free Cities, and soon the talents that he possessed came to the ears of King Aerys II Targaryen, who no longer trusted his son, wife or Hand.

When Tywin Lannister arrived at the gates of King's Landing claiming that he was there to bend the knee, it was Varys that counselled the king to leave the gates closed. Aerys, however, opened them on the recommendation of Grand Maester Pycelle. Varys was then pardoned by the new king, Robert Baratheon.

Varys claimed to be loyal to the Baratheons, but he also claimed to have sneaked the young baby Aegon Targaryen across the Narrow Sea. He then gave Aegon to Jon Connington, who he kept alive, although he did pretend that the man died. He also acquired Ser Jorah Mormont as one of his spies.